- BioRxiv Biochemistry
- BioRxiv Bioinformatics
- BioRxiv Biophysics
- BioRxiv Cancer Biology
- BioRxiv Pharmacology and Toxicology
- BioRxiv Systems Biology
- BioRxiv Zoology
- by Boncompte, G., Medel, V., Irani, M., Lachaux, J.-P., Ossandon, T.The aperiodic component of brain field potentials, like EEG, LFP and intracortical recordings, has shown to be a valuable tool in basic neuroscience and in clinical applications. Aperiodic activity is modeled as a power law of the power spectral density, with the aperiodic exponent as the key parameter. Part of the interest in this parameter lies in its proposed role as a marker of the balance between excitatory and inhibitory cortical activity. In theory, a perfect power law would imply […]
- by Chen, Q., Zhang, B., Peng, C., Huang, J., Shen, X., Jiang, C.Comprehensive metagenomic sequence classification of diverse environmental samples faces significant computing memory challenges due to exponentially expanding genome databases. Here, we present Kun-peng, featuring a unique ordered 4GB block database design for ultra-efficient resource management, faster processing, and higher accuracy. When benchmarked on mock communities (Amos HiLo, Mixed, and NIST) against Kraken2, Centrifuge, and Sylph. Kun-peng matched Sylph, achieving the highest precision and lowest false-positive rates while demonstrating superior time and memory efficiency among all tested tools. Furthermore, Kun-peng's efficient […]
- by Michel, J., Lehnert, M., Nebel, M., Quandt, D.Arbuscular mycorrhizal fungi (AMF) are amongst the most studied plant symbionts and regularly found in terrestrial plants. However, global estimates of AMF abundance amongst all land plants are difficult because i) the mycorrhizal status of many non-commercial, wild plant species is still unknown ii) numerous plant species engage in facultative symbiosis, meaning that they can, but do not always do, associate with mycorrhiza and iii) mycorrhizal status can vary amongst individuals of one same plant species at one location, as […]
- by zhang, m., Ke, Y., Shang, K., Zhuo, Z., Liu, H., Li, P., Zhao, N., Sha, J., Li, J.Suaeda Salsa (S. salsa), a pioneer species with short and red-purplish plants in the intertidal zones, has significant ecological, economic, recreational and tourism values. Timely monitoring of S. salsa is crucial for understanding its dynamics and sustainable management of coastal wetlands. Hyperspectral satellite offers valuable opportunities due to its detailed spectral information. This study proposed a Suaeda Salsa Hyperspectral Index (SSHI) for S. salsa mapping based on hyperspectral satellite imagery. The SSHI was developed by considering the large within-class spectral […]
- by Zhai, F., Yun, B., Ming, J., Li, B., Yu, T., Liu, X., Wang, X., Chen, Z.-H., Song, C., Zhao, M., Li, J., Liang, A., Zhang, F.Early diagnosis of the colitis-associated colorectal cancer (CRC) is of great significance for improving prognosis and survival rates. However, the clinical used colonoscopy and biopsy methods are invasive and lack of sensitivity at early stage of cancerization. Herein, we present an amplified sensing strategy in the second near-infrared b (NIR-IIb, 1500-1700 nm) window for non-invasive in situ visualization of early cancerization biomarker miRNA-21. A CRC nanosensor composed of Er3+ doped lanthanide nanoparticles, DNAzyme, and IR820 dye is designed as a […]
- by Sharoni, T., Jaimes-Becerra, A., Lewandowska, M., Aharoni, R., Voolstra, C. R., Fine, M., Moran, Y.The cnidarian class Hexacorallia, encompassing stony corals and sea anemones, plays a critical role in marine ecosystems. Coral bleaching, the disruption of the symbiosis between stony corals and zooxanthellate algae, is driven by climate change-induced seawater warming and further exacerbated by pathogenic microbes. However, how pathogens, especially viruses, contribute to accelerated bleaching remains poorly understood. The present study utilizes the model sea anemone Nematostella vectensis to explore these dynamics by creating a transgenic line with a reporter gene regulated by […]
- by Yamano, S., Umeda, Y.Background: We have previously reported that inhalation exposure to titanium dioxide nanoparticles (TiO2 NPs) for 13 weeks causes early pneumoconiosis lesions in the alveolar region of F344 rats. We defined these characteristic lesions as pulmonary dust foci (PDF). In this report, we re-evaluate and detail the histopathological data regarding particle-induced pneumoconiosis lesions, including progressive lesions of the early PDF lesions, that developed in F344 rats exposed TiO2 NPs by whole body inhalation over a period of two years. Methods: Male […]
- by Raineri, E., Esteve Marco, M. A., Esteve-Codina, A.Motivation: Allele-specific methylation (ASM) refers to differential DNA methylation patterns between two alleles at a given locus. This phenomenon is often driven by genetic variants, such as single nucleotide variants (SNVs), which influence methylation in cis by affecting transcription factor or methylation regulator binding, leading to allele-specific differences. Understanding ASM is critical for elucidating gene regulation, as it impacts gene expression and contributes to normal biological variation as well as disease processes, including cancer and autoimmune disorders. Another key driver […]
- by Pop, R. T., Hsieh, P.-H., Belova, T., Mathelier, A., Kuijjer, M. L.The emergence of high-throughput omics technologies has resulted in their wide application to cancer studies, greatly increasing our understanding of the disruptions occurring at different molecular levels. The role of gene regulation as a core driver of biological processes and its role in the development and progression of cancer has been well established. Transcriptional regulation, a crucial aspect of gene regulation, can be represented as a network of interactions between regulators (such as transcription factors) and their target genes. These […]
- by Otwate, P. W., Nampijja, M., Onyango, S. O., Langat, N., Oloo, L., Makhapila, E., Mabongah, J., Odhiambo, B., Owuor, S., Wekulo, P. K.Abstract Objectives Adults, including teachers and parents have an important role in supporting childrens learning and development through play. This paper aimed to explore parents' and teachers' viewpoints and roles on play in promoting early learning and development in children, which has little emphasis in existing studies. Methods This paper employed a cross-sectional study using a mixed-method approach to gather data from preschool teachers (n=96), parents (n=126), and policy implementers (n=6) in Kenya. We used questionnaires, focus group discussions, and […]
- by Buchthal, J., Chory, E. J., Hill, Z., Zhou, Y., Bondage, D., DeAmelio, S., Freeman, J., Jaenisch, R., Markoulaki, S., Marasco, W. A., Telford, S., Esvelt, K. M.Heritable immunization represents a promising approach for controlling infectious diseases by embedding immunity directly into the genomes of wild species that spread human pathogens. Here, we report the genetic engineering of Mus musculus to produce a neutralizing, protective single-chain antibody against Borrelia burgdorferi, the causative agent of Lyme disease. Engineered mice stably produced a LA-2 scFv-albumin fusion protein across multiple generations, demonstrating robust heritability and stability of gene expression. Following sequential challenges with infected and uninfected ticks, heterozygous mice exhibited […]
- by Frolov, D., Ibraev, I., Sedov, I.Promising {Delta}-machine learning approaches aim to correct the values of molecular properties obtained with computationally inexpensive methods to the accuracy of higher levels of theory. Training such models requires datasets containing the results of calculations at several different levels of quantum chemical theory. While several large and chemically diverse datasets have been published, studies in many areas require specialized datasets of structurally related molecules. Chlorinated polycyclic aromatic hydrocarbons (Cl-PAHs), the products of incomplete combustion of organic substances and materials, are […]
- by Ptaszek, A. L., Kratzwald, S., Sagan, F., Migotti, M., Sanchez-Murcia, P. A., Konrat, R., Platzer, G.Understanding weak interactions in protein-ligand complexes is essential for advancing drug design. Here, we combine experimental and quantum mechanical approaches to study the streptavidin-biotin complex, one of the strongest known protein-ligand binders. Using a monomeric streptavidin mutant, we analyze 1H NMR chemical shift perturbations (CSPs) of biotin upon binding, identifying unprecedented upfield shifts of up to -3.2 ppm. Quantum chemical calculations attribute these shifts primarily to aromatic ring currents, with additional contributions from charge transfer effects linked to weak interactions. […]
- by Gallant, J. L., Oliver, M., Winter, M., Eickenberg, M., Dupre la Tour, T.V4 is a key area within the visual processing hierarchy, and it represents features of intermediate complexity. However, no current computational model explains V4 responses under natural conditions. To address this, we developed a new hierarchical convolutional energy (HCE) model reflecting computations thought to occur in areas V1, V2, and V4, but which consists entirely of simple- and complex-like units like those found in V1. In contrast to prior models, the HCE model is trained end-to-end on neurophysiology data, without […]
- by Ucar, M. C., Alsberga, Z., Alanko, J., Sixt, M., Hannezo, E.Cell and tissue movement in development, cancer invasion, and immune response relies on chemical or mechanical guidance cues. In many systems, this behavior is locally guided by self-generated signaling gradients rather than long-range, pre-patterned cues. However, how heterogeneous mixtures of cells interact non-reciprocally and navigate through self-generated gradients remains largely unexplored. Here we introduce a theoretical framework for the self-organized chemotaxis of heterogeneous cell populations. We find that relative chemotactic sensitivity of cell populations controls their long-time coupling and co-migration […]
- by Peroutka-Bigus, N., Brooks, E. J., Ramey, M. E., D'Erasmo, H., Ernest, J. P., Bauman, A. A., Woolhiser, L. K., Savic, R. M., Lenaerts, A. J., Aldridge, B., Sarathy, J. P., Robertson, G. T.By assessing the standard of care regimen for tuberculosis (TB) in BALB/c and C3HeB/FeJ mice, we demonstrate that rifampin, with or without pyrazinamide, is essential to effective bactericidal response and resistance suppression. Potency measurements in an in vitro lipid-rich model and rabbit caseum assay recapitulate the significance of rifampin as a sterilizing agent. These outcomes align with clinical performance, thus emphasizing the value of in vitro predictive tools and murine TB models with human-like pathology.
- by Ghosh, P., Wadsworth, B. C., Terry, L., Evans, T. A.The regulation of midline crossing of axons is of fundamental importance for the proper development of nervous system connectivity in bilaterian animals. A number of conserved axon guidance signaling pathways coordinate to attract or repel axons at the nervous system midline to ensure the proper regulation of midline crossing. The attractive Netrin-Frazzled/DCC (Net-Fra) signaling pathway is widely conserved among bilaterians, but it is not clear whether the mechanisms by which Net and Fra promote midline crossing are also conserved. In […]
- by Shishikura, K., Li, J., Chen, Y., McKnight, N. R., Bustin, K. A., Barr, E. W., Chilkamari, S. R., Ayub, M., Kim, S. W., Lin, Z., Hu, R.-M., Hicks, K., Wang, X., O'Rourke, D. M., Bollinger, J. M., Binder, Z. A., Parsons, W. H., Martemyanov, K. A., Liu, A., Matthews, M. L.The vasodilator hydralazine (HYZ) has been used clinically for ~ 70 years and remains on the World Health Organization's List of Essential Medicines as a therapy for preeclampsia. Despite its longstanding use and the concomitant progress toward a general understanding of vasodilation, the target and mechanism of HYZ have remained unknown. We show that HYZ selectively targets 2-aminoethanethiol dioxygenase (ADO) by chelating its metal cofactor and alkylating one of its ligands. This covalent inactivation slows entry of proteins into the […]
- by Mann, S. G. A., Paz-Galeano, M., Shahsavarani, M., Perley, J. O., Guo, J., Garza-Garcia, J. J. O., Qu, Y.The Apocynaceae family produces a remarkable diversity of monoterpenoid indole alkaloids (MIAs), many of which possess significant pharmaceutical value. Among these, sarpagan and akuammiline alkaloids represent distinct subclasses characterized by their intricate stereochemical frameworks, derived through enzymatically controlled cyclization and rearrangement of the key precursor geissoschizine. In this study, we systematically investigated the products and stereochemical outcomes of sarpagan bridge enzymes (SBEs) and rhazimal synthases (RHS), key enzymes involved in geissoschizine cyclization and MIA diversification. Using two previously characterized enzymes […]
- by Campbell, L., Lowran, K., Cismas, E., Wu, C.Nucleic acid sequences that are rich in guanines can form G-quadruplex (G4) structures, which can impede DNA replication or repair. The FANCJ helicase plays a role in maintaining genomic stability by facilitating DNA replication through regions of DNA that form G4 structures. This activity has been associated with an AKKQ motif in FANCJ and it is thought that this motif retains the ability to also target 8-oxoguanine-modified G4 (8oxoG4) structures. We hypothesize that the molecular recognition of FANCJ AKKQ to […]